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Tools

Six tools for protein-first research over UniProt — discovery search is the entry point, uniprot_map_ids is the bridge that turns any sibling identifier into a UniProtKB accession, and the rest fetch curated records, proteomes, taxonomy, and sequences:

uniprot_search_proteins

Search UniProtKB and return curated protein records — the discovery entry point.

• text_search for plain language (the 80% case) or query for full Lucene field syntax (gene, organism_id, keyword, go, reviewed, protein_name, family, length, existence, accession) — exactly one
• reviewed defaults to true (Swiss-Prot only) so the agent isn't drowned in TrEMBL predictions; set false to include them
• organism_id convenience filter ANDed onto the query
• Optional facets for server-side count breakdowns (e.g. reviewed, model_organism)
• Forward cursor pagination (UniProtKB has no offset paging); totalResults and the effective query echoed back
• Every hit carries reviewed, annotationScore, and proteinExistence so curation quality is weighable

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uniprot_get_entry

Fetch full curated UniProtKB entries by accession in batch — this tool does not search.

• Batch up to 20 accessions in one round trip
• Sectioned record: function, catalytic activity, cofactors, subcellular location, disease, PTMs, natural variants, isoforms, domains, GO terms, keywords, cross-references
• Partial-success output — resolved entries in succeeded[], unknown/withdrawn ones in failed[]; the whole batch never aborts on one bad accession
• fields trims the upstream projection; identity and provenance fields are always retained
• A single oversized record returns kind: "outline" (a section listing) instead of overflowing context — re-call the same accession with sections: [...] to pull only what's needed
• Accessions come from uniprot_search_proteins or uniprot_map_ids; strip any -N isoform suffix first

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uniprot_map_ids

Translate identifiers across databases via UniProt's ID-mapping service — the bridge from any sibling server's identifier into a UniProtKB accession.

• from_db / to_db are validated enums (e.g. Gene_Name, Ensembl, RefSeq_Protein, ChEMBL, PDB, GeneID, UniProtKB_AC-ID) so an unsupported pair fails before the upstream call
• Target UniProtKB-Swiss-Prot for reviewed accessions only (the usual intent), or UniProtKB / UniProtKB_AC-ID to include unreviewed TrEMBL
• The job runs asynchronously; the tool submits it and polls within a budget. A running job returns status: "running" with a ticket — pass that ticket alone to poll the same job
• A completed call returns status: "finished" with one upstream page (up to 500 mappings). If continuation is present, pass it alone to fetch the next completed page without polling or re-submitting; its absence marks the terminal page
• Pair a gene-symbol from_db with tax_id to disambiguate species
• unmappedIds is populated only from UniProt's failedIds, so identifiers UniProt normalizes in successful result rows are not misclassified as failures

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uniprot_get_proteome

Fetch the reference proteome for an organism by UPID or NCBI taxon ID — provide exactly one.

• Metadata inline: proteome type, total protein count, BUSCO completeness (score, complete/fragmented/missing counts, lineage dataset), genome assembly accession
• The protein set is opt-in via include_proteins (it is large — human is ~147,506) and returns a capped page with a forward cursor and truncation disclosure
• Narrow the protein list with the query filter (UniProtKB Lucene syntax) for a subset
• Resolve an organism name to a taxon ID first with uniprot_get_taxonomy

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uniprot_get_taxonomy

Resolve a taxonomy record by NCBI taxon ID or scientific name — provide exactly one.

• Returns scientific and common name, mnemonic, rank, parent, and the full lineage (root → near ancestor)
• include_children fetches the immediate child taxa via a follow-up search (not inline on the record)
• Turns an organism name into the taxon ID that uniprot_search_proteins (organism_id) and uniprot_get_proteome (taxon_id) expect

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uniprot_get_sequence

Fetch the canonical amino-acid sequence (FASTA) for an accession — the cheap, sequence-only path (for the full functional record use uniprot_get_entry).

• Returns the canonical sequence with its length and parsed FASTA header
• include_isoforms also returns the alternatively-spliced isoform sequences
• Accessions come from uniprot_search_proteins or uniprot_map_ids; strip any -N isoform suffix first

Resources and prompts

All resource data is also reachable via tools — tool-only clients lose nothing. UniProtKB is far too large to enumerate, so there is no resource list(); discovery is uniprot_search_proteins's job.

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation
• Unified error handling — handlers throw, framework catches, classifies, and formats
• Pluggable auth: none, jwt, oauth
• Swappable storage backends: in-memory, filesystem, Supabase, Cloudflare KV/R2/D1
• Structured logging with optional OpenTelemetry tracing
• STDIO and Streamable HTTP transports

UniProt-specific:

• Keyless — UniProt REST requires no API key; works against any rest.uniprot.org-compatible base (override UNIPROT_BASE_URL for a private mirror)
• One thin fetch client over all four REST collections (UniProtKB, ID Mapping, Proteomes, Taxonomy) with retry/backoff and HTML-error-page detection
• Batch entry fetch — N accessions in one round trip, cross-referenced against the request to flag any missing
• Async ID-mapping run → poll bounded by a wall-clock budget, with a running-job ticket and separately paginated completed results

Agent-friendly output:

• Provenance is data, not decoration — reviewed, annotationScore, proteinExistence, and per-field PubMed/ECO evidence ship on every record so the agent can weigh manual vs. predicted annotation
• Graceful partial failure — uniprot_get_entry returns per-accession succeeded[] / failed[] rows instead of aborting the batch
• Discriminated output contracts — uniprot_get_entry returns kind: "full" | "outline", while uniprot_map_ids separates a running-job ticket from a finished-page continuation; callers branch on data, not string parsing
• Sparsity preserved — absent upstream fields stay absent, never fabricated (most curated sections are legitimately missing on TrEMBL entries)

Getting started

Public Hosted Instance

A public instance is available at https://uniprot.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "type": "streamable-http",
      "url": "https://uniprot.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

Add the following to your MCP client configuration file. UniProt REST is keyless — no API key required.

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/uniprot-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with npx (no Bun required):

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/uniprot-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/uniprot-mcp-server:latest"]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp

Prerequisites

• Bun v1.3.0 or higher (or Node.js v24+).
• No API key — UniProt REST is keyless and open. Data is UniProt, CC BY 4.0.

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/uniprot-mcp-server.git

2. Navigate into the directory:

cd uniprot-mcp-server

3. Install dependencies:

bun install

Configuration

All configuration is validated at startup via Zod schemas in src/config/server-config.ts. UniProt REST is keyless, so every server-specific variable below is an optional override.

See .env.example for the full list of optional overrides.

Running the server

Local development

• Build and run:

  # One-time build
  bun run rebuild
  
  # Run the built server
  bun run start:stdio
  # or
  bun run start:http
  

• Run checks and tests:

  bun run devcheck   # Lint, format, typecheck, security
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec
  

Docker

docker build -t uniprot-mcp-server .
docker run --rm -e MCP_TRANSPORT_TYPE=stdio ghcr.io/cyanheads/uniprot-mcp-server:latest

The Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/uniprot-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.

Project structure

Development guide

See CLAUDE.md (and the byte-identical AGENTS.md) for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, ctx.state for tenant-scoped storage
• Register new tools and resources in the createApp() arrays
• Wrap the UniProt API: validate raw → normalize to domain type → return the output schema; never fabricate missing fields

Contributing

Issues and pull requests are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.